leonarski_fandClaude Opus 5
e5c0066129
Everything a run determines went to stdout and nowhere else. The space group and the evidence behind it, the error model, the post-refine commit-or-reject decisions and their held-out residuals, the two-pass adopt-or-roll-back, the resolution cut, the merging statistics - all of it scrolled past interleaved with progress lines and was gone. A user who was not watching had no record, and nothing could read it. `rugnux` had no log file at all; the `rugnux.log` in the regression harness is that harness capturing stdout. Write `<prefix>_report.txt` alongside the .cif/.mtz/.hkl, always, with no option to ask for it. It holds what the run DETERMINED; timing, rates, per-image progress and engine chatter stay on stdout, where they belong. Every line rugnux logs was classified result-or-process against the regression corpus to decide what crosses over. The format follows XDS's CORRECT.LP, which has been read by people and parsed by other programs for twenty years: `KEY= value` assignment lines a script greps one at a time, fixed-width tables with stable headers and a total row, `WARNING:` sentences in plain English, section banners. REPORT_VERSION says when that interface last changed. It is assembled from results the pipeline already computed, so an unconditional file costs nothing, and a failure to write it is logged and swallowed - a run that produced good reflections must not be lost to a side file. One thing CORRECT.LP does not have to solve: a rotation run integrates twice and writes both passes, so every report says which pass it describes and why that pass was adopted. `--no-merge` gets a report too, saying MERGE= NOT_PERFORMED rather than leaving a reader to infer it from absent sections. An empty output prefix still writes nothing. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
96 lines
3.8 KiB
C++
96 lines
3.8 KiB
C++
// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <string>
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#include <optional>
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#include <vector>
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#include <map>
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#include <memory>
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#include "../common/DiffractionGeometry.h"
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#include "../common/DiffractionExperiment.h"
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#include "../common/PixelMask.h"
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#include "../common/AzimuthalIntegrationMapping.h"
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struct JFJochReaderDataset {
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std::string arm_date;
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DiffractionExperiment experiment;
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// Shared, not copied, across dataset snapshots: the mask is constant for a run, so a per-frame
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// dataset refresh / mutable copy must not clone the full-detector (~tens of MB) mask. Held as
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// shared_ptr<const>; the rare edit (user mask) builds a fresh mask (copy-on-write). Never null.
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std::shared_ptr<const PixelMask> pixel_mask = std::make_shared<const PixelMask>();
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std::optional<int64_t> error_value;
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// The master file's detect_ice_rings key, kept as written rather than collapsed to a bool, so a
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// consumer can tell "the file asked for this" from "the file said nothing". Offline processing
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// defaults ice handling by geometry when the file is silent (see rugnux_cli).
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std::optional<bool> file_detect_ice_rings;
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std::string jfjoch_release;
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std::vector<float> az_int_bin_to_q;
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std::vector<float> az_int_bin_to_phi;
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size_t azimuthal_bins = 0;
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size_t q_bins = 0;
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std::vector<float> spot_count;
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std::vector<float> spot_count_indexed;
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std::vector<float> spot_count_low_res;
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std::vector<float> spot_count_ice_rings;
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std::vector<float> spot_count_ice_control;
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std::vector<float> indexing_result;
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std::vector<float> indexing_lattice_count;
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std::vector<float> bkg_estimate;
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std::vector<float> ice_ring_score;
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std::vector<float> resolution_estimate;
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std::vector<float> efficiency;
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std::vector<float> profile_radius;
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std::vector<float> mosaicity_deg;
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std::vector<float> b_factor;
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std::vector<float> integrated_reflections;
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std::vector<float> image_scale_factor;
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std::vector<float> image_scale_cc;
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std::vector<int64_t> max_value;
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// Per-image sweep-quality code from /entry/MX/sweepQuality: 0 = the image is in no flagged range,
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// otherwise a 1-based index into sweep_quality_reasons (the vocabulary stored beside it, so the
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// codes read back without this source). Both empty when the file carries no sweep quality, which
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// means the run never looked - not that every image was clean.
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std::vector<uint8_t> sweep_quality;
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std::vector<std::string> sweep_quality_reasons;
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// Maps this dataset's image index -> the original/collected image number it came from.
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// Empty means identity (image i == original image i). Lets a dataset be a subset (or strided
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// selection) of the truly collected images: reprocessing snapshots over a sub-range, and (in
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// future) a main dataset that was filtered on-the-fly during collection.
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std::vector<int> source_image_number;
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std::vector<std::string> roi;
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std::vector<std::vector<int64_t>> roi_sum;
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std::vector<std::vector<int64_t>> roi_sum_sq;
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std::vector<std::vector<int64_t>> roi_max;
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std::vector<std::vector<int64_t>> roi_npixel;
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std::vector<std::vector<float>> roi_x;
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std::vector<std::vector<float>> roi_y;
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// ROI definitions stored in the master file. The logical definitions populate
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// experiment.ROI() (they re-derive with the current geometry); roi_map is the
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// per-pixel bitmask as written (constant footprint), with roi_bit_index mapping
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// each ROI name to its bit.
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std::vector<uint16_t> roi_map;
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std::map<std::string, uint16_t> roi_bit_index;
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std::vector<std::string> calibration_data;
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JFJochReaderDataset() = default;
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JFJochReaderDataset(const JFJochReaderDataset &other) = default;
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};
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